plot heatmap from the raw hic file(get from the juicer)

[ChenDepp]

@sa501428
hi.
I want to get the matrix from the hic file, arrange and orient the contig (including forward and reverse) based on the order defined by myself to get a new matrix , then use the matrix plot the heatmap.
i write a python script based on the hicstraw api. the script as below

i found sometimes the matrix_numpy shape is (1,1), i don't how to get the matrix corrrectly. please tell me how to get it.
waiting your reply.
thanks

[lidaof]

Hi @ChenDepp you probably need to @sa501428 for your question. I most time use the JS version of straw...not sure about the python version. Sorry for that.

[ChenDepp]

@lidaof hi thanks you very much.

[MahdiSayadSadr]

Hi,

We have an interactive notebook going through straw on Python, which I think could help you with your issue! Let me know if you still have trouble! https://colab.research.google.com/drive/1-GG-n-p9nZ7Be82UVJG7n3Q_wQ9IeuFN?usp=sharing#scrollTo=xf8HUdMVWAgQ